\docType{class}
\name{annotationByFeature-class}
\alias{annotationByFeature}
\alias{annotationByFeature-class}
\title{An S4 class for  overlap of target features with a generic annotation}
\description{
  This object is desgined to hold statistics and
  information about genomic feature overlaps it extends
  \code{\link{list}} class.
}
\section{Slots}{
  \describe{ \item{\code{members}}{a matrix showing overlap
  of target features with annotation genomic features}
  \item{\code{annotation}}{a named vector of percentages of
  overlap between feature and annotation}'
  \item{\code{precedence}}{a named vector of percentages of
  overlap between feature and annotation}
  \item{\code{num.annotation}}{a named vector of numbers of
  overlap between feature and annotation}
  \item{\code{num.precedence}}{a named vector of numbers of
  overlap between feature and annotation}
  \item{\code{no.of.OlapFeat}}{vector}
  \item{\code{perc.of.OlapFeat}}{vector} }
}
\examples{
data(methylKit)
cpg.obj=read.feature.flank(system.file("extdata", "cpgi.hg18.bed.txt", package = "methylKit"),feature.flank.name=c("CpGi","shores"))

# the following function returns annotationByFeature object
ann=annotate.WithFeature.Flank(methylDiff.obj,cpg.obj$CpGi,cpg.obj$shores,feature.name="CpGi",flank.name="Shores")
ann
}
\seealso{
  see \code{\link[methylKit]{annotate.WithFeature.Flank}}
  and \code{\link[methylKit]{annotate.WithFeature}} on how
  to create this object.  see following functions that
  operates on this object:
  \code{\link[methylKit]{getMembers}},
  \code{\link[methylKit]{getTargetAnnotationStats}},
  \code{\link[methylKit]{getFeatsWithTargetsStats}},
  \code{\link[methylKit]{plotTargetAnnotation}}
}

